# Generated by roxygen2: do not edit by hand

export(classifyStrandMode)
export(filterBAMtx)
export(filterBAMtxFlag)
export(gDNAdx)
export(gDNAtx)
export(identifyStrandMode)
export(plotAlnOrigins)
export(plotFrgLength)
export(strnessByFeature)
export(testBAMtxFlag)
exportClasses(gDNAx)
exportMethods("strandMode<-")
exportMethods(allStrandModes)
exportMethods(getDx)
exportMethods(getIgc)
exportMethods(getInt)
exportMethods(plot)
exportMethods(show)
exportMethods(singleEnd)
exportMethods(strandMode)
exportMethods(strandedness)
importFrom(AnnotationDbi,select)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,query)
importFrom(BiocGenerics,basename)
importFrom(BiocGenerics,path)
importFrom(BiocGenerics,species)
importFrom(BiocParallel,"bpprogressbar<-")
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,multicoreWorkers)
importFrom(Biostrings,encoding)
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,genomeStyles)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicAlignments,"strandMode<-")
importFrom(GenomicAlignments,GAlignments)
importFrom(GenomicAlignments,encodeOverlaps)
importFrom(GenomicAlignments,findOverlaps)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,granges)
importFrom(GenomicAlignments,invertStrand)
importFrom(GenomicAlignments,isCompatibleWithSkippedExons)
importFrom(GenomicAlignments,isCompatibleWithSplicing)
importFrom(GenomicAlignments,last)
importFrom(GenomicAlignments,njunc)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,readGAlignmentsList)
importFrom(GenomicAlignments,strandMode)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,pmapToTranscripts)
importFrom(GenomicFiles,reduceByYield)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,grglist)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,match)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,trim)
importFrom(GenomicRanges,width)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IRanges)
importFrom(IRanges,IntegerList)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(IRanges,coverage)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,lapply)
importFrom(IRanges,reduce)
importFrom(IRanges,relist)
importFrom(IRanges,resize)
importFrom(IRanges,slidingWindows)
importFrom(IRanges,viewSums)
importFrom(IRanges,width)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,"asMates<-")
importFrom(Rsamtools,"bamWhat<-")
importFrom(Rsamtools,"yieldSize<-")
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asMates)
importFrom(Rsamtools,bamTag)
importFrom(Rsamtools,bamWhat)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,isOpen)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,sortBam)
importFrom(Rsamtools,testPairedEndBam)
importFrom(Rsamtools,yieldSize)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,FilterRules)
importFrom(S4Vectors,Hits)
importFrom(S4Vectors,countQueryHits)
importFrom(S4Vectors,countSubjectHits)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,from)
importFrom(S4Vectors,isSingleNumber)
importFrom(S4Vectors,isSorted)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,nLnode)
importFrom(S4Vectors,nRnode)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,to)
importFrom(S4Vectors,unname)
importFrom(S4Vectors,unstrsplit)
importFrom(Seqinfo,"genome<-")
importFrom(Seqinfo,"seqinfo<-")
importFrom(Seqinfo,genome)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(bitops,bitAnd)
importFrom(cli,cli_abort)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_progress_bar)
importFrom(cli,cli_progress_done)
importFrom(cli,cli_progress_update)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,grid)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(matrixStats,rowMins)
importFrom(methods,as)
importFrom(methods,formalArgs)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(plotrix,thigmophobe)
importFrom(stats,binom.test)
importFrom(stats,density)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,pbinom)
importFrom(stats,setNames)
importFrom(utils,installed.packages)
